Development of the computing system Jana

Václav Petříček, Michal Dušek, Lukáš Palatinus

Jana is a crystallographic computing system focused to solution, refinement and interpretation of difficult, namely modulated structures. Modulated structures can be described with up to three modulation vectors and their diffraction data (from x-ray, electron or neutron sources) can be based on single crystal as well as powder samples.

The program enables arbitrary combination of the input diffraction data. Typical example is a combination of neutron powder data with x-ray single crystal data of the same compound because both diffraction methods have a different sensitivity to various structure features. For solution of the phase problem Charge flipping is available (program Superflip distributed together with Jana system), but the program can also communicate with another external programs utilizing direct methods via a simple interface.

Jana can calculate crystal structure of multiphase systems, merohedric and pseudomerohedric twins, twins with partial overlaps of diffraction spots, commensurate and composite (intergrowth) structures. It contains sophisticated transformation tools for complete transformation of the studied system to a lower symmetry, to a multiple unit cell and also possibility to transform automatically a commensurate structure to a three-dimensional supercell. Variety of user constraints and restraints is available as well as a tool for refinement molecular structures in a rigid body approximation, possibility to introduce a local symmetry and a lot of another possibilities. The program has around 1500 registered user (registration is optional) and it is almost solely used for calculation of modulated structures.

The current development of Jana runs in the framework of Praemium Academiae, an award obtained by the main authors of the program, Václav Petříček, in 2008. The long-term aim is to integrate all widely used crystallographuc methods into one system and create a universal tool for calculation of any crystal structure except proteins. There are three direction in the current development of Jana system:

• Development of the user interface and of the basic procedures towards intuitive and simple way of use. The aim is to reach a simplicity sufficient for using th eprogram like a teaching tool at basic crystallographic courses.
• Development of magnetic structures refinement. This kind of material undergo a magnetic phase transition at very low temperatures leading to an ordering of magnetic moments which gives rise to magnetic satellites. These reflection can only be beasured with neutron diffraction which leads to necessity to combine imprecise neutron diffraction data with x-ray data in order to refine simultaneously the nuclear and magnetic structure. The formalism developed for modulated structures should be also used for magnetic structures because the magnetic satellites can be incommensurate with the translation periodicity of the nuclear structure.
• Development of tools supporting electron diffraction for the project Electron diffractometer (see Research subjects of the department) with the aim to enable refinement of precession electron diffraction data.

Users and citations of Jana. Black line - cumulated number of registered users with an active e-mail address; red line - citations during the given year.

The principal author of the program Jana, Václav Petříček, illuminated by computer monitor.

Web page of Jana2006

Workshops on Jana2006